3F64 | pdb_00003f64

F17a-G lectin domain with bound GlcNAc(beta1-O)paranitrophenyl ligand


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 
    0.248 (Depositor), 0.250 (DCC) 
  • R-Value Work: 
    0.204 (Depositor), 0.209 (DCC) 
  • R-Value Observed: 
    0.206 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 3F64

Ligand Structure Quality Assessment 


This is version 1.7 of the entry. See complete history

Literature

Structural Sampling of Glycan Interaction Profiles Reveals Mucosal Receptors for Fimbrial Adhesins of Enterotoxigenic Escherichia coli.

Lonardi, E.Moonens, K.Buts, L.de Boer, A.R.Olsson, J.D.Weiss, M.S.Fabre, E.Guerardel, Y.Deelder, A.M.Oscarson, S.Wuhrer, M.Bouckaert, J.

(2013) Biology (Basel) 2: 894-917

  • DOI: https://doi.org/10.3390/biology2030894
  • Primary Citation Related Structures: 
    3F64, 3F6J, 3FFO, 4BWO, 4K0O

  • PubMed Abstract: 

    Fimbriae are long, proteinaceous adhesion organelles expressed on the bacterial envelope, evolutionarily adapted by Escherichia coli strains for the colonization of epithelial linings. Using glycan arrays of the Consortium for Functional Glycomics (CFG), the lectin domains were screened of the fimbrial adhesins F17G and FedF from enterotoxigenic E. coli (ETEC) and of the FimH adhesin from uropathogenic E. coli. This has led to the discovery of a more specific receptor for F17G, GlcNAcb1,3Gal. No significant differences emerged from the glycan binding profiles of the F17G lectin domains from five different E. coli strains. However, strain-dependent amino acid variations, predominantly towards the positively charged arginine, were indicated by sulfate binding in FedF and F17G crystal structures. For FedF, no significant binders could be observed on the CFG glycan array. Hence, a shotgun array was generated from microvilli scrapings of the distal jejunum of a 3-week old piglet about to be weaned. On this array, the blood group A type 1 hexasaccharide emerged as a receptor for the FedF lectin domain and remarkably also for F18-fimbriated E. coli. F17G was found to selectively recognize glycan species with a terminal GlcNAc, typifying intestinal mucins. In conclusion, F17G and FedF recognize long glycan sequences that could only be identified using the shotgun approach. Interestingly, ETEC strains display a large capacity to adapt their fimbrial adhesins to ecological niches via charge-driven interactions, congruent with binding to thick mucosal surfaces displaying an acidic gradient along the intestinal tract.


  • Organizational Affiliation
    • Center for Proteomics and Metabolomics, Leiden University Medical Center, P.O. Box 9600, RC Leiden 2300, The Netherlands. e.lonardi@lumc.nl.

Macromolecule Content 

  • Total Structure Weight: 19.39 kDa 
  • Atom Count: 1,461 
  • Modeled Residue Count: 168 
  • Deposited Residue Count: 177 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
F17a-G177Escherichia coliMutation(s): 0 
UniProt
Find proteins for Q99003 (Escherichia coli)
Explore Q99003 
Go to UniProtKB:  Q99003
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ99003
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
LEC

Query on LEC



Download:Ideal Coordinates CCD File
B [auth A]4-nitrophenyl 2-acetamido-2-deoxy-beta-D-glucopyranoside
C14 H18 N2 O8
OMRLTNCLYHKQCK-DHGKCCLASA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free:  0.248 (Depositor), 0.250 (DCC) 
  • R-Value Work:  0.204 (Depositor), 0.209 (DCC) 
  • R-Value Observed: 0.206 (Depositor) 
Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.025α = 90
b = 43.025β = 90
c = 288.45γ = 120
Software Package:
Software NamePurpose
MAR345data collection
CNSrefinement
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2009-11-10
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2013-08-28
    Changes: Database references
  • Version 1.3: 2017-10-25
    Changes: Refinement description
  • Version 1.4: 2020-01-01
    Changes: Data collection, Database references
  • Version 1.5: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Derived calculations, Structure summary
  • Version 1.6: 2023-11-01
    Changes: Data collection, Database references, Refinement description, Structure summary
  • Version 1.7: 2024-11-20
    Changes: Structure summary